Systems Biology

  1. Network Biology
    1. Graph Theory Applications
      1. Network Representation
        1. Adjacency Matrices
          1. Edge Lists
            1. Graph Objects
            2. Network Properties
              1. Degree Distribution
                1. Clustering Coefficient
                  1. Path Length
                    1. Centrality Measures
                      1. Degree Centrality
                        1. Betweenness Centrality
                          1. Closeness Centrality
                            1. Eigenvector Centrality
                          2. Network Motifs and Modules
                            1. Common Network Motifs
                              1. Module Detection Algorithms
                                1. Functional Module Analysis
                              2. Biological Network Types
                                1. Gene Regulatory Networks
                                  1. Transcription Factor Networks
                                    1. Regulatory Motifs
                                      1. Network Inference Methods
                                      2. Protein Interaction Networks
                                        1. Physical Interaction Networks
                                          1. Functional Association Networks
                                            1. Protein Complex Detection
                                            2. Metabolic Networks
                                              1. Reaction Networks
                                                1. Enzyme Networks
                                                  1. Metabolic Pathway Analysis
                                                  2. Signaling Networks
                                                    1. Signal Transduction Pathways
                                                      1. Crosstalk Analysis
                                                        1. Dynamic Signaling Models
                                                      2. Network Analysis Methods
                                                        1. Network Inference
                                                          1. Correlation-Based Methods
                                                            1. Mutual Information
                                                              1. Bayesian Networks
                                                                1. Gaussian Graphical Models
                                                                2. Network Comparison
                                                                  1. Network Alignment
                                                                    1. Network Similarity Metrics
                                                                      1. Differential Network Analysis
                                                                      2. Dynamic Network Analysis
                                                                        1. Time-Varying Networks
                                                                          1. Network Evolution
                                                                            1. Temporal Network Motifs

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                                                                        4. Bioinformatics and Data Analysis

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                                                                        6. Mathematical Modeling